mmg_233_2013_genetics_genomicswikiaorg-20200214-history
GWAS Identifies a Novel Risk Loci for Type 2 Diabetes
Type 2 Diabetes Type 2 Diabetes Mellitis (T2DM), also known as adult-inset diabetes, is the most common form of diabetes, and is characterized by hyperglycemia due to relative deficiency of insulin, known as insulin resistance. This insulin resistance occurs due to destruction of islet cells in the pancreas. Common symptoms associated with Type 2 Diabetes include excess thirst, frequent urination, and constant hunger. The main cause of type 2 diabetes is obesity in those who are genetically predisposed to the disase. Most can manage type 2 diabetes by making dietary changes and increasing the amount of exercise that they engage in. If these changes do not adequately lower blood glucose, medications metformin or insulin may be necessary. When an individual does administer insulin, they must routinely check their blood sugar levels (1). http://cnx.org/content/m46685/latest/ How a Genome-Wide Association Study works: GWAS Wikia A GWAS Indentifies Novel Risk Loci for Type 2 Diabetes (2) Researchers at McGill University in Montreal tested 392,935 single-nucleotide polymorphisms in a French case-control cohort. Markers with the most significant difference in genotype frequencies between cases of type 2 diabetes control were then tested in a second cohort, identifying 4 loci containing variants that confer type 2 diabetes risk. The first loci was the known associative TCF7L2 gene, which has already been implicated in association with type 2 diabetes in multiple populations. The novel loci include: - A non-synonymous polymorphism in the zinc transporter SLC20A8 (expressed only in insulin-producing Beta cells - Two linkage disequilibrium blocks IDE-KIF11_HHEX and EXT2-ALX4 (potentially involved in beta-cell development or function) Together, these results explain a large portion of disease risk and are proof that the genome-wide approach is effective for complex traits such as Diabetes, which has strong genetic and environmental causative agents. Study Design and Analysis This study was a 2-stage GWAS used to identify additional T2DM susceptibility loci. In the first stage, they obtained genotypes from 392,935 single-nucleotide polymorphisms in 1,363 T2DM cases and controls. Genotypes for each subject were obtained using two platforms: Illumina Infinium Human1 Bead Arrays (assay 109,365 SNPs chosen using a gene-centered design) and Human Hap300 BeadArrays (assay 317,503 SNPs chosen to tag haplotype blocks identified by the Phase I HapMap). Of the 409,927 markers that passed quality control, genotypes were obtained for an average of 99.2% (Human1) and 99.4% (Hap300) of markers for each subject with a reproducibility of >99.9%. In total, T2DM association was tested for 100,764 (human1) and 309,163 (Hap300) SNPs representing 392,935 unique loci (Figure 1). Because there were unequal numbers of males and females in the study, 12,666 sex-chromosome SNPs were analyzed separately for each gender. Markers were selected for assessment in the second cohort using significance thresholds on the basis of the divergence between the observed and expected P-values. These included 28 autosomal SNPs from the Human1 chip and 43 autosomal SNPs from the Hap300 chip for a total of 66 unique SNPs representing 44 unique loci. The stage 1 results included the known association with the TCF7L2 SNP rs7903146 and several other SNPs at that locus also illustrated Genome-wide significance after correcting for 392,935 tests. 59 SNPs were then prioritized from stage 1 due to significant T2DM association, including one of the eight significant TCF7L2 markers. Genotypes for the 57 SNPs were obtained from 2,617 cases and 2,894 controls, and the SNPs were analyzed in the same way as they were in stage 1. Of the 57 SNPs tested in stage 2, 8 SNPs representing 5 unique loci showed significant association based on P-values calculated using 10 million permutations of the disease state labels (Table 1). Following this association, the Wald Test (3 ) was used to assess the effects of age, sex, and BMI on the association between the markers and T2DM. A wald test is used when a relationship exists within or between data items and is used to test the true value of the parameter based on the sample estimate. The wald test showed that none of the 8 associations was substantially changed by considering the effects of these characteristics. Identification of the 4 novel loci Fast-track stage 2 genotyping confirmed the reported association for TCF7L2 (rs7903146) on chromosome 10, and in addition identified significant associations for 7 SNPs representing 4 novel loci (table 1, above). The most significant association corresponds to rs13266634, a non-synonymous SNP in SLC30A8, located in a 33-kb linkage disequilibrium block on chromosome 8 containing only the 3' end of this gene (Figure 2A). SLC30A8 encodes a zinc transporter expressed only in the secretory vesicles of beta-cells of the pancreas, and has involvment in the final stages of insulin biosynthesis, in which co-crystallization with zinc occurs. Another study illustrated that overexpression of SLC30A8 in insulinoma cells resulted in increased glucose-stimulated insulin secretion. Because a lack of SLC30A8 would be causative of decreased insulin secretion by insulinoma cells, which would lead to hyperglycemia similarly associated with T2DM, possible dietary implications or therapeutic agents with zinc supplementation may be beneficial for T2DM. SNPs rs1111875 and rs7923837 are located near the telomeric end of a 270-kb linkage disequilibrium block on chromosome 10 (Figure 2B). This linkage disequilibrium block encodes two genes of known significance: 1. Insulin-degrading enzyme (IDE): reduces amyloid accumulation and thus amylin-mediated cytotoxicity in beta cells and also was found to increase insulin resistance in mice when ablated. 2. Homeodomain Protein (HHEX): a target of the Wnt-signalling pathway and is essential for pancreatic development This linkage disequilibrium block also encodes a kinesin-interacting factor 11 (KIF11). Two more loci were also found. The first involves 3 SNPs within introns of exostatin2 (EXT2) at the telomeric end of a linkage disequilibrium block on chromosome 11q (Figure 2C). EXT2 modulates hedgehog signalling, a pathway involved in early pancreatic development and the regulation of insulin synthesis. This block also was found to contain ALX4, a homeodomain protein with possible involvement in the Wnt signalling pathway. A final T2DM associated SNP in chromosome 11 was found and is currently identified as "LOC387761". Quantification of the Contribution of Loci to T2DM To do this, the population attributable risk (PAR) was calculated for each marker (Table 1). Stepwise logistic regression showed that one SNP per locus explains the entire effect of the locus and that there was no significant epistaxis between loci. Therefore, it was calculated that the PAR for the novel 4 loci together with TCF7L2 is 70%. Conclusions The T2DM risk loci that were identified by this study involve genes implicated in pancreatic development and the control of insulin secretion. Also, these loci may also affect the peripheral response to insulin, suggesting a more complex combination of multiple genes associated with characteristics common in T2DM. This study has medical importance because they have identified unexpected contributors to T2DM that may be useful in developing targeted therapeutics towards. References 1. http://en.wikipedia.org/wiki/Diabetes_mellitus_type_2 2. http://www.nature.com.ezproxy.uvm.edu/nature/journal/v445/n7130/full/nature05616.html 3. The Wald Test (wikipedia): http://en.wikipedia.org/wiki/Wald_test 4. Pancreas Diagram: http://cnx.org/content/m46685/latest/